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<td valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial">&nbsp;<br><big><big><strong><a href="src.html"><font color="#ffffff">src</font></a>.structures</strong></big></big> (28 February 2006)</font></td
><td align=right valign=bottom
><font color="#ffffff" face="helvetica, arial"><a href=".">index</a><br><a href="file:/user/yhuang/pdb2pqr/trunk/pdb2pqr/src/structures.py">/user/yhuang/pdb2pqr/trunk/pdb2pqr/src/structures.py</a></font></td></tr></table>
    <p><tt>Structures&nbsp;for&nbsp;PDB2PQR<br>
&nbsp;<br>
This&nbsp;module&nbsp;contains&nbsp;the&nbsp;structure&nbsp;objects&nbsp;used&nbsp;in&nbsp;PDB2PQR&nbsp;and&nbsp;their<br>
associated&nbsp;methods.<br>
&nbsp;<br>
----------------------------<br>
&nbsp;<br>
PDB2PQR&nbsp;--&nbsp;An&nbsp;automated&nbsp;pipeline&nbsp;for&nbsp;the&nbsp;setup,&nbsp;execution,&nbsp;and&nbsp;analysis&nbsp;of<br>
Poisson-Boltzmann&nbsp;electrostatics&nbsp;calculations<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;Copyright&nbsp;(c)&nbsp;2002-2010,&nbsp;Jens&nbsp;Erik&nbsp;Nielsen,&nbsp;University&nbsp;College&nbsp;Dublin;&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;Nathan&nbsp;A.&nbsp;Baker,&nbsp;Washington&nbsp;University&nbsp;in&nbsp;St.&nbsp;Louis;&nbsp;Paul&nbsp;Czodrowski&nbsp;&amp;&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;Gerhard&nbsp;Klebe,&nbsp;University&nbsp;of&nbsp;Marburg<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;All&nbsp;rights&nbsp;reserved.<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;Redistribution&nbsp;and&nbsp;use&nbsp;in&nbsp;source&nbsp;and&nbsp;binary&nbsp;forms,&nbsp;with&nbsp;or&nbsp;without&nbsp;modification,&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;are&nbsp;permitted&nbsp;provided&nbsp;that&nbsp;the&nbsp;following&nbsp;conditions&nbsp;are&nbsp;met:<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*&nbsp;Redistributions&nbsp;of&nbsp;source&nbsp;code&nbsp;must&nbsp;retain&nbsp;the&nbsp;above&nbsp;copyright&nbsp;notice,&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;this&nbsp;list&nbsp;of&nbsp;conditions&nbsp;and&nbsp;the&nbsp;following&nbsp;disclaimer.<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*&nbsp;Redistributions&nbsp;in&nbsp;binary&nbsp;form&nbsp;must&nbsp;reproduce&nbsp;the&nbsp;above&nbsp;copyright&nbsp;notice,&nbsp;<br>
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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;and/or&nbsp;other&nbsp;materials&nbsp;provided&nbsp;with&nbsp;the&nbsp;distribution.<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*&nbsp;Neither&nbsp;the&nbsp;names&nbsp;of&nbsp;University&nbsp;College&nbsp;Dublin,&nbsp;Washington&nbsp;University&nbsp;in&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;St.&nbsp;Louis,&nbsp;or&nbsp;University&nbsp;of&nbsp;Marburg&nbsp;nor&nbsp;the&nbsp;names&nbsp;of&nbsp;its&nbsp;contributors&nbsp;may&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;be&nbsp;used&nbsp;to&nbsp;endorse&nbsp;or&nbsp;promote&nbsp;products&nbsp;derived&nbsp;from&nbsp;this&nbsp;software&nbsp;without&nbsp;<br>
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&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;THIS&nbsp;SOFTWARE&nbsp;IS&nbsp;PROVIDED&nbsp;BY&nbsp;THE&nbsp;COPYRIGHT&nbsp;HOLDERS&nbsp;AND&nbsp;CONTRIBUTORS&nbsp;"AS&nbsp;IS"&nbsp;AND&nbsp;<br>
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&nbsp;&nbsp;&nbsp;&nbsp;WARRANTIES&nbsp;OF&nbsp;MERCHANTABILITY&nbsp;AND&nbsp;FITNESS&nbsp;FOR&nbsp;A&nbsp;PARTICULAR&nbsp;PURPOSE&nbsp;ARE&nbsp;DISCLAIMED.&nbsp;<br>
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&nbsp;&nbsp;&nbsp;&nbsp;OR&nbsp;OTHERWISE)&nbsp;ARISING&nbsp;IN&nbsp;ANY&nbsp;WAY&nbsp;OUT&nbsp;OF&nbsp;THE&nbsp;USE&nbsp;OF&nbsp;THIS&nbsp;SOFTWARE,&nbsp;EVEN&nbsp;IF&nbsp;ADVISED&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;OF&nbsp;THE&nbsp;POSSIBILITY&nbsp;OF&nbsp;SUCH&nbsp;DAMAGE.<br>
&nbsp;<br>
----------------------------</tt></p>
<p>
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<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Modules</strong></big></font></td></tr>
    
<tr><td bgcolor="#aa55cc"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%"><table width="100%" summary="list"><tr><td width="25%" valign=top><a href="copy.html">copy</a><br>
<a href="math.html">math</a><br>
</td><td width="25%" valign=top><a href="os.html">os</a><br>
<a href="string.html">string</a><br>
</td><td width="25%" valign=top><a href="sys.html">sys</a><br>
</td><td width="25%" valign=top></td></tr></table></td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ee77aa">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Classes</strong></big></font></td></tr>
    
<tr><td bgcolor="#ee77aa"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%"><dl>
<dt><font face="helvetica, arial"><a href="src.pdb.html#ATOM">src.pdb.ATOM</a>
</font></dt><dd>
<dl>
<dt><font face="helvetica, arial"><a href="src.structures.html#Atom">Atom</a>
</font></dt></dl>
</dd>
<dt><font face="helvetica, arial"><a href="src.structures.html#Chain">Chain</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.structures.html#Residue">Residue</a>
</font></dt></dl>
 <p>
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<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="Atom">class <strong>Atom</strong></a>(<a href="src.pdb.html#ATOM">src.pdb.ATOM</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Class&nbsp;<a href="#Atom">Atom</a><br>
&nbsp;<br>
The&nbsp;<a href="#Atom">Atom</a>&nbsp;class&nbsp;inherits&nbsp;off&nbsp;the&nbsp;<a href="src.pdb.html#ATOM">ATOM</a>&nbsp;object&nbsp;in&nbsp;pdb.py.&nbsp;&nbsp;It&nbsp;is&nbsp;used<br>
for&nbsp;adding&nbsp;fields&nbsp;not&nbsp;found&nbsp;in&nbsp;the&nbsp;pdb&nbsp;that&nbsp;may&nbsp;be&nbsp;useful&nbsp;for&nbsp;analysis.<br>
Also&nbsp;simplifies&nbsp;code&nbsp;by&nbsp;combining&nbsp;<a href="src.pdb.html#ATOM">ATOM</a>&nbsp;and&nbsp;HETATM&nbsp;objects&nbsp;into&nbsp;a<br>
single&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="Atom-__init__"><strong>__init__</strong></a>(self, atom, type, residue)</dt><dd><tt>Initialize&nbsp;the&nbsp;new&nbsp;<a href="#Atom">Atom</a>&nbsp;object&nbsp;by&nbsp;using&nbsp;the&nbsp;old&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom:&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;original&nbsp;<a href="src.pdb.html#ATOM">ATOM</a>&nbsp;object&nbsp;(<a href="src.pdb.html#ATOM">ATOM</a>)<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;Either&nbsp;<a href="src.pdb.html#ATOM">ATOM</a>&nbsp;or&nbsp;HETATM&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;residue:&nbsp;A&nbsp;pointer&nbsp;back&nbsp;to&nbsp;the&nbsp;parent&nbsp;residue&nbsp;object&nbsp;(<a href="#Residue">Residue</a>)</tt></dd></dl>

<dl><dt><a name="Atom-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Returns&nbsp;a&nbsp;string&nbsp;of&nbsp;the&nbsp;new&nbsp;atom&nbsp;type.&nbsp;&nbsp;Uses&nbsp;the&nbsp;<a href="src.pdb.html#ATOM">ATOM</a>&nbsp;string<br>
output&nbsp;but&nbsp;changes&nbsp;the&nbsp;first&nbsp;field&nbsp;to&nbsp;either&nbsp;by&nbsp;<a href="src.pdb.html#ATOM">ATOM</a>&nbsp;or<br>
HETATM&nbsp;as&nbsp;necessary.<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;str:&nbsp;String&nbsp;with&nbsp;<a href="src.pdb.html#ATOM">ATOM</a>/HETATM&nbsp;field&nbsp;set&nbsp;appropriately</tt></dd></dl>

<dl><dt><a name="Atom-addBond"><strong>addBond</strong></a>(self, bondedatom)</dt><dd><tt>Add&nbsp;a&nbsp;bond&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;bonds<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;bondedatom:&nbsp;The&nbsp;atom&nbsp;to&nbsp;bond&nbsp;to&nbsp;(<a href="#Atom">Atom</a>)</tt></dd></dl>

<dl><dt><a name="Atom-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="#Atom">Atom</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;of&nbsp;<a href="#Atom">Atom</a>&nbsp;(either&nbsp;<a href="src.pdb.html#ATOM">ATOM</a>&nbsp;or&nbsp;HETATM)<br>
&nbsp;&nbsp;&nbsp;&nbsp;serial:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="#Atom">Atom</a>&nbsp;serial&nbsp;number<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="#Atom">Atom</a>&nbsp;name<br>
&nbsp;&nbsp;&nbsp;&nbsp;altLoc:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Alternate&nbsp;location<br>
&nbsp;&nbsp;&nbsp;&nbsp;resName:&nbsp;&nbsp;&nbsp;&nbsp;<a href="#Residue">Residue</a>&nbsp;name<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;<a href="#Chain">Chain</a>&nbsp;identifier<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="#Residue">Residue</a>&nbsp;sequence&nbsp;number<br>
&nbsp;&nbsp;&nbsp;&nbsp;iCode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Code&nbsp;for&nbsp;insertion&nbsp;of&nbsp;residues<br>
&nbsp;&nbsp;&nbsp;&nbsp;x:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Orthogonal&nbsp;coordinates&nbsp;for&nbsp;X&nbsp;in&nbsp;Angstroms.<br>
&nbsp;&nbsp;&nbsp;&nbsp;y:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Orthogonal&nbsp;coordinates&nbsp;for&nbsp;Y&nbsp;in&nbsp;Angstroms.<br>
&nbsp;&nbsp;&nbsp;&nbsp;z:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Orthogonal&nbsp;coordinates&nbsp;for&nbsp;Z&nbsp;in&nbsp;Angstroms.<br>
&nbsp;&nbsp;&nbsp;&nbsp;occupancy:&nbsp;&nbsp;Occupancy<br>
&nbsp;&nbsp;&nbsp;&nbsp;tempFactor:&nbsp;Temperature&nbsp;Factor<br>
&nbsp;&nbsp;&nbsp;&nbsp;segID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Segment&nbsp;identifier<br>
&nbsp;&nbsp;&nbsp;&nbsp;element:&nbsp;&nbsp;&nbsp;&nbsp;Element&nbsp;symbol<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Charge&nbsp;on&nbsp;the&nbsp;atom<br>
&nbsp;&nbsp;&nbsp;&nbsp;bonds:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;bonds&nbsp;associated&nbsp;with&nbsp;the&nbsp;atom<br>
&nbsp;&nbsp;&nbsp;&nbsp;interbonds:&nbsp;The&nbsp;intrabonds&nbsp;associated&nbsp;with&nbsp;the&nbsp;atom<br>
&nbsp;&nbsp;&nbsp;&nbsp;extrabonds:&nbsp;The&nbsp;extrabonds&nbsp;assocaited&nbsp;with&nbsp;the&nbsp;atom<br>
&nbsp;&nbsp;&nbsp;&nbsp;residue:&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;parent&nbsp;residue&nbsp;of&nbsp;the&nbsp;atom<br>
&nbsp;&nbsp;&nbsp;&nbsp;radius:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;radius&nbsp;of&nbsp;the&nbsp;atom<br>
&nbsp;&nbsp;&nbsp;&nbsp;ffcharge:&nbsp;&nbsp;&nbsp;The&nbsp;forcefield&nbsp;charge&nbsp;on&nbsp;the&nbsp;atom<br>
&nbsp;&nbsp;&nbsp;&nbsp;hdonor:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Whether&nbsp;the&nbsp;atom&nbsp;is&nbsp;a&nbsp;hydrogen&nbsp;donor<br>
&nbsp;&nbsp;&nbsp;&nbsp;hacceptor:&nbsp;&nbsp;Whether&nbsp;the&nbsp;atom&nbsp;is&nbsp;a&nbsp;hydrogen&nbsp;acceptor<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="Atom-getCoords"><strong>getCoords</strong></a>(self)</dt><dd><tt>Return&nbsp;the&nbsp;x,y,z&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;in&nbsp;list&nbsp;form<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;the&nbsp;coordinates&nbsp;(list)</tt></dd></dl>

<dl><dt><a name="Atom-hasReference"><strong>hasReference</strong></a>(self)</dt><dd><tt>Determine&nbsp;if&nbsp;the&nbsp;atom&nbsp;object&nbsp;has&nbsp;a&nbsp;reference&nbsp;object&nbsp;or&nbsp;not.<br>
All&nbsp;known&nbsp;atoms&nbsp;should&nbsp;have&nbsp;reference&nbsp;objects.<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;atom&nbsp;has&nbsp;a&nbsp;reference&nbsp;object,&nbsp;0&nbsp;otherwise.</tt></dd></dl>

<dl><dt><a name="Atom-isBackbone"><strong>isBackbone</strong></a>(self)</dt><dd><tt>Return&nbsp;true&nbsp;if&nbsp;atom&nbsp;name&nbsp;is&nbsp;in&nbsp;backbone,&nbsp;otherwise&nbsp;false<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;state:&nbsp;1&nbsp;if&nbsp;true,&nbsp;0&nbsp;if&nbsp;false</tt></dd></dl>

<dl><dt><a name="Atom-isHydrogen"><strong>isHydrogen</strong></a>(self)</dt><dd><tt>Is&nbsp;this&nbsp;atom&nbsp;a&nbsp;Hydrogen&nbsp;atom?<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;1&nbsp;if&nbsp;<a href="#Atom">Atom</a>&nbsp;is&nbsp;a&nbsp;Hydrogen,&nbsp;0&nbsp;otherwise</tt></dd></dl>

<dl><dt><a name="Atom-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="#Atom">Atom</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;to&nbsp;set&nbsp;the&nbsp;member&nbsp;to<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;of&nbsp;<a href="#Atom">Atom</a>&nbsp;(either&nbsp;<a href="src.pdb.html#ATOM">ATOM</a>&nbsp;or&nbsp;HETATM)<br>
&nbsp;&nbsp;&nbsp;&nbsp;serial:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="#Atom">Atom</a>&nbsp;serial&nbsp;number<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="#Atom">Atom</a>&nbsp;name<br>
&nbsp;&nbsp;&nbsp;&nbsp;altLoc:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Alternate&nbsp;location<br>
&nbsp;&nbsp;&nbsp;&nbsp;resName:&nbsp;&nbsp;&nbsp;&nbsp;<a href="#Residue">Residue</a>&nbsp;name<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;<a href="#Chain">Chain</a>&nbsp;identifier<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="#Residue">Residue</a>&nbsp;sequence&nbsp;number<br>
&nbsp;&nbsp;&nbsp;&nbsp;iCode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Code&nbsp;for&nbsp;insertion&nbsp;of&nbsp;residues<br>
&nbsp;&nbsp;&nbsp;&nbsp;x:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Orthogonal&nbsp;coordinates&nbsp;for&nbsp;X&nbsp;in&nbsp;Angstroms.<br>
&nbsp;&nbsp;&nbsp;&nbsp;y:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Orthogonal&nbsp;coordinates&nbsp;for&nbsp;Y&nbsp;in&nbsp;Angstroms.<br>
&nbsp;&nbsp;&nbsp;&nbsp;z:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Orthogonal&nbsp;coordinates&nbsp;for&nbsp;Z&nbsp;in&nbsp;Angstroms.<br>
&nbsp;&nbsp;&nbsp;&nbsp;occupancy:&nbsp;&nbsp;Occupancy<br>
&nbsp;&nbsp;&nbsp;&nbsp;tempFactor:&nbsp;Temperature&nbsp;Factor<br>
&nbsp;&nbsp;&nbsp;&nbsp;segID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Segment&nbsp;identifier<br>
&nbsp;&nbsp;&nbsp;&nbsp;element:&nbsp;&nbsp;&nbsp;&nbsp;Element&nbsp;symbol<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Charge&nbsp;on&nbsp;the&nbsp;atom<br>
&nbsp;&nbsp;&nbsp;&nbsp;residue:&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;parent&nbsp;residue&nbsp;of&nbsp;the&nbsp;atom<br>
&nbsp;&nbsp;&nbsp;&nbsp;radius:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;radius&nbsp;of&nbsp;the&nbsp;atom<br>
&nbsp;&nbsp;&nbsp;&nbsp;ffcharge:&nbsp;&nbsp;&nbsp;The&nbsp;forcefield&nbsp;charge&nbsp;on&nbsp;the&nbsp;atom<br>
&nbsp;&nbsp;&nbsp;&nbsp;hdonor:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Whether&nbsp;the&nbsp;atom&nbsp;is&nbsp;a&nbsp;hydrogen&nbsp;donor<br>
&nbsp;&nbsp;&nbsp;&nbsp;hacceptor:&nbsp;&nbsp;Whether&nbsp;the&nbsp;atom&nbsp;is&nbsp;a&nbsp;hydrogen&nbsp;acceptor<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="Chain">class <strong>Chain</strong></a></font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt><a href="#Chain">Chain</a>&nbsp;class<br>
&nbsp;<br>
The&nbsp;chain&nbsp;class&nbsp;contains&nbsp;information&nbsp;about&nbsp;each&nbsp;chain&nbsp;within&nbsp;a&nbsp;given<br>
Protein&nbsp;object.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="Chain-__init__"><strong>__init__</strong></a>(self, chainID)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;The&nbsp;chainID&nbsp;for&nbsp;this&nbsp;chain&nbsp;as&nbsp;denoted&nbsp;in<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;the&nbsp;PDB&nbsp;file&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="Chain-addResidue"><strong>addResidue</strong></a>(self, residue)</dt><dd><tt>Add&nbsp;a&nbsp;residue&nbsp;to&nbsp;the&nbsp;chain<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;residue:&nbsp;The&nbsp;residue&nbsp;to&nbsp;be&nbsp;added&nbsp;(<a href="#Residue">Residue</a>)</tt></dd></dl>

<dl><dt><a name="Chain-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="#Chain">Chain</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;ID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;ID&nbsp;of&nbsp;the&nbsp;chain<br>
&nbsp;&nbsp;&nbsp;&nbsp;Residues:&nbsp;The&nbsp;list&nbsp;of&nbsp;residues&nbsp;within&nbsp;the&nbsp;<a href="#Chain">Chain</a><br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="Chain-getAtoms"><strong>getAtoms</strong></a>(self)</dt><dd><tt>Return&nbsp;a&nbsp;list&nbsp;of&nbsp;<a href="#Atom">Atom</a>&nbsp;objects&nbsp;contained&nbsp;in&nbsp;this&nbsp;chain<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomlist:&nbsp;List&nbsp;of&nbsp;<a href="#Atom">Atom</a>&nbsp;objects&nbsp;(list)</tt></dd></dl>

<dl><dt><a name="Chain-getResidues"><strong>getResidues</strong></a>(self)</dt><dd><tt>Return&nbsp;a&nbsp;list&nbsp;of&nbsp;<a href="#Residue">Residue</a>&nbsp;objects&nbsp;in&nbsp;this&nbsp;chain</tt></dd></dl>

<dl><dt><a name="Chain-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;chain<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;chain&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="Chain-numResidues"><strong>numResidues</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;residues&nbsp;for&nbsp;the&nbsp;chain<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;residues&nbsp;in&nbsp;the&nbsp;chain&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="Chain-renumberResidues"><strong>renumberResidues</strong></a>(self)</dt><dd><tt>Renumber&nbsp;Atoms&nbsp;based&nbsp;on&nbsp;actual&nbsp;<a href="#Residue">Residue</a>&nbsp;number&nbsp;and&nbsp;not&nbsp;PDB&nbsp;resSeq</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="Residue">class <strong>Residue</strong></a></font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt><a href="#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
The&nbsp;residue&nbsp;class&nbsp;contains&nbsp;a&nbsp;list&nbsp;of&nbsp;<a href="#Atom">Atom</a>&nbsp;objects&nbsp;associated&nbsp;with&nbsp;that<br>
residue&nbsp;and&nbsp;other&nbsp;helper&nbsp;functions.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="Residue-__init__"><strong>__init__</strong></a>(self, atoms)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A&nbsp;list&nbsp;of&nbsp;<a href="#Atom">Atom</a>&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<dl><dt><a name="Residue-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="Residue-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Add&nbsp;the&nbsp;atom&nbsp;object&nbsp;to&nbsp;the&nbsp;residue.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom:&nbsp;The&nbsp;object&nbsp;to&nbsp;be&nbsp;added&nbsp;(<a href="src.pdb.html#ATOM">ATOM</a>)</tt></dd></dl>

<dl><dt><a name="Residue-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="Residue-createAtom"><strong>createAtom</strong></a>(self, name, newcoords, type)</dt><dd><tt>Add&nbsp;a&nbsp;new&nbsp;atom&nbsp;object&nbsp;to&nbsp;the&nbsp;residue.&nbsp;Uses&nbsp;an&nbsp;atom<br>
currently&nbsp;in&nbsp;the&nbsp;residue&nbsp;to&nbsp;seed&nbsp;the&nbsp;new&nbsp;atom<br>
object,&nbsp;then&nbsp;replaces&nbsp;the&nbsp;coordinates&nbsp;and&nbsp;name&nbsp;accordingly.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;new&nbsp;atom&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;x,y,z&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;new&nbsp;atom&nbsp;(list)<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;of&nbsp;atom,&nbsp;<a href="src.pdb.html#ATOM">ATOM</a>&nbsp;or&nbsp;HETATM</tt></dd></dl>

<dl><dt><a name="Residue-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="Residue-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="Residue-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="Residue-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="Residue-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="Residue-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="Residue-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="Residue-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="Residue-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="Residue-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;C,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="Residue-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="Residue-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="Residue-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="Residue-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="Residue-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="Residue-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table></td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#55aa55">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Data</strong></big></font></td></tr>
    
<tr><td bgcolor="#55aa55"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%"><strong>BACKBONE</strong> = ['N', 'CA', 'C', 'O', 'O2', 'HA', 'HN', 'H', 'tN']<br>
<strong>DIHEDRAL</strong> = 57.2958<br>
<strong>SMALL</strong> = 9.9999999999999995e-08<br>
<strong>__author__</strong> = 'Todd Dolinsky'<br>
<strong>__date__</strong> = '28 February 2006'</td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#7799ee">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Author</strong></big></font></td></tr>
    
<tr><td bgcolor="#7799ee"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%">Todd&nbsp;Dolinsky</td></tr></table>
</body></html>